One of the most profound effects of the Bert Cates trial was that it established that freedom of thought is one of the most basic elements that define human consciousness. The interplay between Drummond and Brady reveals one of the lasting effects of the trial as the right to think:

The individual human mind... An idea is a greater monument than a cathedral. And the advance of man’s knowledge is more of a miracle than any sticks turned to snakes, or the parting of waters!

One of the effects of the Bert Cates trial was to examine what it was to be a human being who thinks. It is seen as one of the most elemental constructions of human consciousness. Cates is on trial because he sought to challenge the Hillsboro law that forbade teaching an alternate theory to cosmological reality. At the end of the trial, the ability to think is validated as one of the fundamental elements which define what it means to be human.

Another related effect of the Cates trial is the examination of what defines truth. Matthew Brady, Reverend Brown, and other members who side or embrace the prosecution wish to posit one construction of truth. This vision is rather narrow, reductive and dogmatic. However, in the trial, Drummond brings forth the idea that the search for truth might be complex and intricate, causing individuals to question the world and their place in it:

All shine, and no substance! [Turning to Cates] Bert, whenever you see something bright, shining, perfect-seeming—all gold, with purple spots—look behind the paint! And if it’s a lie—show it up for what it really is!

One of the lasting effects of the trial is that the conventional and unquestioned nature of truth is revealed as something that might be "all gold, with purple spots." The ability to question what truth is and construct it for one self and to "show it up for what it really is" becomes one of the lasting effects of the Cates trial.